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Yorodumi- PDB-1emb: GREEN FLUORESCENT PROTEIN (GFP) FROM AEQUOREA VICTORIA, GLN 80 RE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1emb | ||||||
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Title | GREEN FLUORESCENT PROTEIN (GFP) FROM AEQUOREA VICTORIA, GLN 80 REPLACED WITH ARG | ||||||
Components | GREEN FLUORESCENT PROTEIN | ||||||
Keywords | FLUORESCENT PROTEIN / BETA-BARREL | ||||||
Function / homology | Function and homology information serine-type endopeptidase inhibitor activity / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Brejc, K. / Sixma, T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1997 Title: Structural basis for dual excitation and photoisomerization of the Aequorea victoria green fluorescent protein. Authors: Brejc, K. / Sixma, T.K. / Kitts, P.A. / Kain, S.R. / Tsien, R.Y. / Ormo, M. / Remington, S.J. #1: Journal: Science / Year: 1996 Title: Crystal Structure of the Aequorea Victoria Green Fluorescent Protein Authors: Ormo, M. / Cubitt, A.B. / Kallio, K. / Gross, L.A. / Tsien, R.Y. / Remington, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1emb.cif.gz | 55.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1emb.ent.gz | 43.1 KB | Display | PDB format |
PDBx/mmJSON format | 1emb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1emb_validation.pdf.gz | 426.2 KB | Display | wwPDB validaton report |
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Full document | 1emb_full_validation.pdf.gz | 434.6 KB | Display | |
Data in XML | 1emb_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 1emb_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/1emb ftp://data.pdbj.org/pub/pdb/validation_reports/em/1emb | HTTPS FTP |
-Related structure data
Related structure data | 1emaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26945.383 Da / Num. of mol.: 1 / Mutation: Q80R Source method: isolated from a genetically manipulated source Details: CHROMOPHORE CONTAINING PROTEIN 65 - 67 DENOTED AS CRO Source: (gene. exp.) Aequorea victoria (jellyfish) / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42212 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 3.8 Details: PROTEIN WAS CRYSTALLIZED FROM 50 MM KH2PO4 AND 20 % (W/V) PEG 8000, PH 3.8. | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1995 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→20 Å / Num. obs: 13001 / % possible obs: 91.3 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Rsym value: 0.061 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.13→2.2 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.186 / % possible all: 54.5 |
Reflection | *PLUS Num. measured all: 60182 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS Lowest resolution: 2.2 Å / % possible obs: 54.5 % / Rmerge(I) obs: 0.186 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EMA Resolution: 2.13→20 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Bsol: 145.5 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.196 / Rfactor Rfree: 0.254 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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